!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_KinaciHaskinsSevik_2012_BNC__MO_105008013807_000 Supported species : B C N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = B (Configuration in file "config-F-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.284182587307686 Forces: 1 -2.94215118e+00 6.84178631e+00 -7.90358105e+00 2 -3.44014398e+00 -1.74029620e+00 -6.61538633e-01 3 -2.73674858e+00 -7.12021523e-01 6.25568088e+00 4 5.70604545e+00 -7.37266874e+00 -1.03541986e+00 5 6.41581406e-02 1.16681307e+00 7.70555917e-01 6 -1.26414151e+00 -1.36998937e-02 -6.82687305e-01 7 1.82831741e+00 1.13427102e+00 1.29134757e-01 8 1.15625569e+01 2.16266086e+00 -2.57457653e+00 9 -5.16463775e-01 5.94621442e-01 1.17801318e+00 10 -2.61767002e-01 2.15947823e-01 1.06313242e-01 11 1.55231635e+00 2.00191122e+00 -4.70472888e+00 12 1.19550803e+00 -7.28775984e-01 -1.95284551e+00 13 -3.12110609e+00 8.22951838e-01 -1.26715788e-01 14 -1.59262335e+00 -8.01016457e-01 7.86231717e-01 15 2.49061546e+01 -1.03383718e+01 -2.24545165e+01 16 -4.32648790e+00 -1.16439186e+01 2.32664335e+01 17 -1.70540246e+00 6.00851415e+00 -5.76002610e+00 18 -6.93498430e+00 -3.63578666e+00 8.07031230e+00 19 9.36316834e+00 9.20963864e-01 2.63000341e+00 20 5.28623577e-01 -1.09727845e+00 -1.38606260e+00 21 -7.03733499e-02 2.52107164e+00 1.66920932e+00 22 1.46800702e-03 -1.07849560e+00 7.05581764e-01 23 -7.50533286e-01 6.54854317e-01 -9.13346115e-01 24 8.78995863e-01 -2.37835289e+00 4.72166043e-01 25 -3.49216313e+00 -3.23655216e-01 6.88974619e+00 26 -4.36647926e-02 -1.14960734e+00 8.66807816e-01 27 -2.50965007e+00 5.63710047e+00 1.08430303e+00 28 1.49572303e+00 -8.96287392e-01 -1.27433454e+00 29 -1.38185499e+01 1.63222098e+01 -8.04945614e+00 30 -1.02011833e+01 -4.80234319e+00 5.33964449e+00 31 -9.85294374e-01 1.32647375e+00 -5.15092100e-01 32 1.63039660e+00 3.80424294e-01 -2.25209921e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = B (Configuration in file "config-T-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.284182587307686 Forces: 1 -2.94215118e+00 6.84178631e+00 -7.90358105e+00 2 -3.44014398e+00 -1.74029620e+00 -6.61538633e-01 3 -2.73674858e+00 -7.12021523e-01 6.25568088e+00 4 5.70604545e+00 -7.37266874e+00 -1.03541986e+00 5 6.41581406e-02 1.16681307e+00 7.70555917e-01 6 -1.26414151e+00 -1.36998937e-02 -6.82687305e-01 7 1.82831741e+00 1.13427102e+00 1.29134757e-01 8 1.15625569e+01 2.16266086e+00 -2.57457653e+00 9 -5.16463775e-01 5.94621442e-01 1.17801318e+00 10 -2.61767002e-01 2.15947823e-01 1.06313242e-01 11 1.55231635e+00 2.00191122e+00 -4.70472888e+00 12 1.19550803e+00 -7.28775984e-01 -1.95284551e+00 13 -3.12110609e+00 8.22951838e-01 -1.26715788e-01 14 -1.59262335e+00 -8.01016457e-01 7.86231717e-01 15 2.49061546e+01 -1.03383718e+01 -2.24545165e+01 16 -4.32648790e+00 -1.16439186e+01 2.32664335e+01 17 -1.70540246e+00 6.00851415e+00 -5.76002610e+00 18 -6.93498430e+00 -3.63578666e+00 8.07031230e+00 19 9.36316834e+00 9.20963864e-01 2.63000341e+00 20 5.28623577e-01 -1.09727845e+00 -1.38606260e+00 21 -7.03733499e-02 2.52107164e+00 1.66920932e+00 22 1.46800702e-03 -1.07849560e+00 7.05581764e-01 23 -7.50533286e-01 6.54854317e-01 -9.13346115e-01 24 8.78995863e-01 -2.37835289e+00 4.72166043e-01 25 -3.49216313e+00 -3.23655216e-01 6.88974619e+00 26 -4.36647926e-02 -1.14960734e+00 8.66807816e-01 27 -2.50965007e+00 5.63710047e+00 1.08430303e+00 28 1.49572303e+00 -8.96287392e-01 -1.27433454e+00 29 -1.38185499e+01 1.63222098e+01 -8.04945614e+00 30 -1.02011833e+01 -4.80234319e+00 5.33964449e+00 31 -9.85294374e-01 1.32647375e+00 -5.15092100e-01 32 1.63039660e+00 3.80424294e-01 -2.25209921e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 174.69004354361533 Forces: 1 -1.98121737e+01 -1.30037829e+01 -1.46838004e+01 2 -3.89123797e+01 -4.47154586e+01 -5.64538848e+01 3 1.22003154e+01 -4.80652088e+01 -4.04381293e+01 4 -3.23801483e+01 -4.39297532e+01 2.61232199e+01 5 1.10656555e+01 -1.34466095e+01 -4.86551265e+00 6 1.63179223e+01 1.53099115e+01 -8.21229610e+01 7 1.16940478e+01 -3.67673169e+01 4.54819471e+01 8 2.68752955e+01 -3.19316680e+01 -4.53379629e+00 9 -1.13992984e+01 -1.52889474e+01 -9.75698094e+01 10 5.90916361e+01 3.86023482e+01 -3.99520611e+01 11 -3.44756653e+01 5.44821256e+01 -4.77622919e+00 12 -6.91878105e+01 4.41746839e+01 3.29052700e+01 13 5.44162477e+01 4.79061882e+01 -3.62232205e+01 14 1.25464202e+01 1.51179873e+01 -1.40480471e+01 15 5.24988453e+01 -2.35150823e+01 -4.26924482e+01 16 -2.37360235e+01 6.47934669e+01 -3.13731307e+01 17 -4.65316798e+01 -2.95117368e+01 2.18046047e+01 18 -2.33434160e+01 1.78782965e+01 5.00168664e+01 19 -1.36025642e+00 -1.12534232e+01 1.35437765e+01 20 -2.13437408e+00 3.21786647e+00 5.32194206e+00 21 1.73412995e+01 -3.62177972e+01 1.54775490e+01 22 2.75159960e+01 -5.46711460e+00 2.88358420e+01 23 3.22714212e+01 -2.22981141e+01 1.40541156e+01 24 -1.84518113e+01 1.93729870e+01 1.10206629e+01 25 -3.13934672e+01 -5.79498349e+00 3.19198182e+01 26 3.81611257e+01 2.21722091e+01 -1.12555930e+01 27 -5.39083174e+00 -1.81734991e+01 2.16369435e+01 28 -4.47767036e+01 1.21254163e+01 3.13119676e+01 29 -2.17091848e+01 -2.31221893e+01 6.03642632e+01 30 3.77864710e+01 6.18563798e+01 2.59783129e+01 31 1.61645230e+01 -1.20040928e+01 3.26327739e+01 32 -9.51997562e-01 1.74969114e+01 1.25587484e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 174.69004354361533 Forces: 1 -1.98121737e+01 -1.30037829e+01 -1.46838004e+01 2 -3.89123797e+01 -4.47154586e+01 -5.64538848e+01 3 1.22003154e+01 -4.80652088e+01 -4.04381293e+01 4 -3.23801483e+01 -4.39297532e+01 2.61232199e+01 5 1.10656555e+01 -1.34466095e+01 -4.86551265e+00 6 1.63179223e+01 1.53099115e+01 -8.21229610e+01 7 1.16940478e+01 -3.67673169e+01 4.54819471e+01 8 2.68752955e+01 -3.19316680e+01 -4.53379629e+00 9 -1.13992984e+01 -1.52889474e+01 -9.75698094e+01 10 5.90916361e+01 3.86023482e+01 -3.99520611e+01 11 -3.44756653e+01 5.44821256e+01 -4.77622919e+00 12 -6.91878105e+01 4.41746839e+01 3.29052700e+01 13 5.44162477e+01 4.79061882e+01 -3.62232205e+01 14 1.25464202e+01 1.51179873e+01 -1.40480471e+01 15 5.24988453e+01 -2.35150823e+01 -4.26924482e+01 16 -2.37360235e+01 6.47934669e+01 -3.13731307e+01 17 -4.65316798e+01 -2.95117368e+01 2.18046047e+01 18 -2.33434160e+01 1.78782965e+01 5.00168664e+01 19 -1.36025642e+00 -1.12534232e+01 1.35437765e+01 20 -2.13437408e+00 3.21786647e+00 5.32194206e+00 21 1.73412995e+01 -3.62177972e+01 1.54775490e+01 22 2.75159960e+01 -5.46711460e+00 2.88358420e+01 23 3.22714212e+01 -2.22981141e+01 1.40541156e+01 24 -1.84518113e+01 1.93729870e+01 1.10206629e+01 25 -3.13934672e+01 -5.79498349e+00 3.19198182e+01 26 3.81611257e+01 2.21722091e+01 -1.12555930e+01 27 -5.39083174e+00 -1.81734991e+01 2.16369435e+01 28 -4.47767036e+01 1.21254163e+01 3.13119676e+01 29 -2.17091848e+01 -2.31221893e+01 6.03642632e+01 30 3.77864710e+01 6.18563798e+01 2.59783129e+01 31 1.61645230e+01 -1.20040928e+01 3.26327739e+01 32 -9.51997562e-01 1.74969114e+01 1.25587484e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -31.123380622062932 Forces: 1 3.59267403e-01 3.41673476e-01 1.00174864e+00 2 -5.49418375e-01 6.01906285e-01 -3.31613961e-01 3 -5.45974832e-01 7.85051880e-01 -1.04337048e+00 4 6.14129172e-01 -2.97427919e-01 -2.29581706e-01 5 -2.91081390e-01 1.18375422e+00 1.10139898e+00 6 -9.83092753e-01 -1.93590345e-01 1.07009508e+00 7 -5.03601398e-01 1.21538125e+00 6.33792854e-01 8 2.56969515e-01 -9.06023724e-01 3.35449551e-01 9 1.16579592e+00 -3.13005753e-01 6.88102234e-01 10 -5.11759646e-01 -1.06227983e+00 5.28997748e-01 11 -3.46298978e-01 3.66009760e-01 -2.01578242e-01 12 -6.16402728e-01 -9.00189041e-01 -4.06249189e-02 13 -2.25863597e-01 3.94405313e-01 4.54963418e-01 14 -3.67872872e-01 -7.01203768e-01 1.20425757e+00 15 -4.62887604e-01 1.10154848e+00 -4.72217484e-01 16 1.60517409e+00 -1.00598877e+00 -3.16871796e-01 17 1.41036973e+00 1.12447568e+00 9.77014850e-02 18 -5.28821490e-01 -3.45522526e-01 -3.19038127e-03 19 -2.62327988e-01 1.02175068e+00 4.41764400e-02 20 1.13838081e+00 -6.95696686e-02 -1.35169087e+00 21 4.32600242e-01 8.02252577e-01 7.85431745e-01 22 -6.76386778e-01 -7.69804008e-01 -5.09192064e-01 23 -9.20672151e-01 6.88565789e-01 -1.36374088e+00 24 5.11554304e-01 -6.48466541e-01 -1.20159108e+00 25 1.20223042e+00 5.75680974e-01 4.15254644e-01 26 1.86722521e-01 -8.42821818e-01 1.33436546e+00 27 -7.03022379e-01 4.46996904e-01 -1.19595522e+00 28 8.72604181e-01 -1.02005769e+00 -8.48867163e-01 29 5.60375527e-01 3.62277690e-01 6.39770137e-01 30 -8.66211252e-01 -1.23664237e+00 1.61507389e-01 31 -1.14923729e+00 3.78368674e-01 -6.06447100e-01 32 1.94759669e-01 -1.07750586e+00 -7.80480020e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -31.123380622062932 Forces: 1 3.59267403e-01 3.41673476e-01 1.00174864e+00 2 -5.49418375e-01 6.01906285e-01 -3.31613961e-01 3 -5.45974832e-01 7.85051880e-01 -1.04337048e+00 4 6.14129172e-01 -2.97427919e-01 -2.29581706e-01 5 -2.91081390e-01 1.18375422e+00 1.10139898e+00 6 -9.83092753e-01 -1.93590345e-01 1.07009508e+00 7 -5.03601398e-01 1.21538125e+00 6.33792854e-01 8 2.56969515e-01 -9.06023724e-01 3.35449551e-01 9 1.16579592e+00 -3.13005753e-01 6.88102234e-01 10 -5.11759646e-01 -1.06227983e+00 5.28997748e-01 11 -3.46298978e-01 3.66009760e-01 -2.01578242e-01 12 -6.16402728e-01 -9.00189041e-01 -4.06249189e-02 13 -2.25863597e-01 3.94405313e-01 4.54963418e-01 14 -3.67872872e-01 -7.01203768e-01 1.20425757e+00 15 -4.62887604e-01 1.10154848e+00 -4.72217484e-01 16 1.60517409e+00 -1.00598877e+00 -3.16871796e-01 17 1.41036973e+00 1.12447568e+00 9.77014850e-02 18 -5.28821490e-01 -3.45522526e-01 -3.19038127e-03 19 -2.62327988e-01 1.02175068e+00 4.41764400e-02 20 1.13838081e+00 -6.95696686e-02 -1.35169087e+00 21 4.32600242e-01 8.02252577e-01 7.85431745e-01 22 -6.76386778e-01 -7.69804008e-01 -5.09192064e-01 23 -9.20672151e-01 6.88565789e-01 -1.36374088e+00 24 5.11554304e-01 -6.48466541e-01 -1.20159108e+00 25 1.20223042e+00 5.75680974e-01 4.15254644e-01 26 1.86722521e-01 -8.42821818e-01 1.33436546e+00 27 -7.03022379e-01 4.46996904e-01 -1.19595522e+00 28 8.72604181e-01 -1.02005769e+00 -8.48867163e-01 29 5.60375527e-01 3.62277690e-01 6.39770137e-01 30 -8.66211252e-01 -1.23664237e+00 1.61507389e-01 31 -1.14923729e+00 3.78368674e-01 -6.06447100e-01 32 1.94759669e-01 -1.07750586e+00 -7.80480020e-01 MIXED STRUCTURE (pbc=False)-- Species = B C N (Configuration in file "config-F-BCN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 144.72562424199367 Forces: 1 -1.67834036e+01 -5.73771794e+01 -5.45225242e+01 2 2.16799381e+01 1.68609926e+01 -5.29648551e+01 3 4.39270069e+01 -7.55524495e+01 -6.70613046e+01 4 -8.04501244e+01 1.14129236e+01 6.45263783e+01 5 -8.47000388e+00 -2.70440166e+01 -4.21300555e+01 6 2.30781116e+01 2.25035542e+01 -3.68972615e+01 7 3.62213054e+01 -2.70210919e+01 -1.45068307e+01 8 9.80221142e+01 -7.20935670e+01 3.12047348e+01 9 4.95284542e+00 4.60882212e+01 -4.25755614e+01 10 -2.84783408e+01 3.21065561e+01 -6.20242501e+00 11 -1.47622920e+02 6.64578576e+01 -2.12178065e+01 12 -1.33478403e+00 1.25535907e-01 -1.21554607e+00 13 4.26393397e+01 -1.89757641e+01 -5.63298981e+01 14 1.86738901e+01 1.01717759e+01 -1.62196524e+01 15 3.42451597e+01 -1.41288911e+01 1.90576207e+01 16 -8.45170682e-01 5.31306366e+01 6.18876522e+00 17 -5.99278077e+01 -2.80159652e+01 4.46333958e+01 18 1.94025462e+01 4.69626984e+01 7.14546907e+01 19 2.87271259e+00 -3.97476544e+00 4.01268653e+00 20 -3.19494691e+01 -3.16615385e+01 2.79803347e+01 21 -3.79698413e+01 -5.91602479e+01 3.53064023e+01 22 4.73873640e+01 3.50901498e+01 3.15291561e+01 23 6.68016896e+00 -8.51714973e+00 1.42672438e+01 24 3.42459281e+01 -6.35388295e+01 4.61525099e+00 25 -1.25749970e+01 3.26033471e+01 -1.62055556e+01 26 -1.22620195e+01 5.10316316e+00 -4.51889506e+00 27 -2.46508396e+01 5.86506720e+01 3.78894415e+01 28 -2.22175579e-01 3.32667178e-01 1.38551177e-01 29 -1.83931970e+00 6.10653461e+00 1.07789155e+01 30 2.57544499e+01 2.28489784e+01 -8.38077678e+00 31 3.20096454e+01 -2.51579528e+01 2.28914075e+01 32 -2.64113096e+01 4.56631443e+01 1.44739729e+01 MIXED STRUCTURE (pbc=True)-- Species = B C N (Configuration in file "config-T-BCN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 209.80113789264033 Forces: 1 -1.30627842e+01 -6.41544315e+01 -5.79734011e+01 2 8.19185693e+00 7.24255457e+00 -1.83031758e+01 3 4.73630613e+01 -7.39546631e+01 -6.84348827e+01 4 -4.63108994e+01 1.12483550e+01 6.96337017e+01 5 3.36144045e+00 -2.55754993e+01 -3.35116240e+01 6 -2.06411388e+00 2.10478506e+01 -3.74890212e+01 7 3.29684046e+01 -2.08279229e+01 -1.79135204e+01 8 9.71372213e+01 -7.22505076e+01 3.22320823e+01 9 8.59561589e+00 5.37157747e+01 -3.82392169e+01 10 -3.03744434e+01 2.99006237e+01 -4.11891027e+00 11 -1.43202612e+02 6.58963814e+01 -7.25201804e+00 12 1.02998798e+01 -1.57645591e+01 -8.51945490e-01 13 4.28271001e+01 -1.47731394e+01 -3.71228200e+01 14 1.92059809e+01 2.06263069e+01 -3.29304966e+00 15 2.76851314e+01 -1.27568581e+01 2.18295356e+01 16 -2.58513554e+00 3.05040378e+01 3.54995359e+00 17 -6.38635777e+01 -4.89886970e+00 5.34037451e+01 18 2.27630629e+01 6.88400603e+01 6.91142563e+01 19 -2.17273070e+00 -1.53138544e+01 -3.69052789e+00 20 -3.13525097e+01 -2.39957470e+01 1.50013339e+01 21 -4.83150315e+01 -4.23635351e+01 3.98334318e+01 22 2.47250468e+01 4.84737858e+01 3.16965465e+01 23 9.32588092e+00 -1.78582137e+00 1.80700131e+01 24 3.20295460e+01 -6.30242380e+01 -1.00046566e+01 25 -1.73812335e+00 3.60262068e+01 -1.61237135e+01 26 -5.11203416e+00 -1.90598545e+01 -3.47846138e+00 27 -2.06409371e+01 7.79241215e+01 -3.43755427e+00 28 3.19282046e+00 5.03738516e+00 -1.23388569e+00 29 -7.81561834e-01 7.75548093e+00 9.88015125e+00 30 2.43726282e+01 -1.17750716e+01 -1.15390077e+01 31 3.04997170e+01 -3.97944200e+01 -2.08570068e+00 32 -3.29679005e+01 3.78300674e+01 1.18523420e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819514== Memcheck, a memory error detector ==1819514== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819514== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819514== Command: python runner2.py Tersoff_LAMMPS_KinaciHaskinsSevik_2012_BNC__MO_105008013807_000 ==1819514== ==1820794== Warning: invalid file descriptor 1024 in syscall close() ==1820794== Warning: invalid file descriptor 1025 in syscall close() ==1820794== Warning: invalid file descriptor 1026 in syscall close() ==1820794== Warning: invalid file descriptor 1027 in syscall close() ==1820794== Use --log-fd= to select an alternative log fd. ==1820794== Warning: invalid file descriptor 1028 in syscall close() ==1820794== Warning: invalid file descriptor 1029 in syscall close() ==1819514== ==1819514== HEAP SUMMARY: ==1819514== in use at exit: 2,262,239 bytes in 1,708 blocks ==1819514== total heap usage: 115,049 allocs, 113,341 frees, 71,548,018 bytes allocated ==1819514== ==1819514== LEAK SUMMARY: ==1819514== definitely lost: 0 bytes in 0 blocks ==1819514== indirectly lost: 0 bytes in 0 blocks ==1819514== possibly lost: 180,827 bytes in 103 blocks ==1819514== still reachable: 2,081,380 bytes in 1,604 blocks ==1819514== of which reachable via heuristic: ==1819514== stdstring : 38 bytes in 1 blocks ==1819514== suppressed: 32 bytes in 1 blocks ==1819514== Rerun with --leak-check=full to see details of leaked memory ==1819514== ==1819514== For lists of detected and suppressed errors, rerun with: -s ==1819514== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8315 from 571) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected.